ncbi
Datasets
All datasets matching “ncbi”ncbi-genbank-complete
Dataset Card for NCBI GenBank Complete
Dataset Summary
GenBank® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank is part of the International Nucleotide Sequence Database Collaboration (INSDC), which comprises the DNA DataBank of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank at NCBI. These three organizations exchange data on a daily basis.
This dataset has been processed into a… See the full description on the dataset page: https://huggingface.co/datasets/pulmo/ncbi-genbank-complete.ncbi-refseq-complete
Dataset Card for NCBI RefSeq Complete
Dataset Summary
The NCBI Reference Sequence (RefSeq) complete dataset provides a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. It serves as a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses.
This dataset has been processed into a… See the full description on the dataset page: https://huggingface.co/datasets/huggingworld/ncbi-refseq-complete.ncbi_diseaseThis paper presents the disease name and concept annotations of the NCBI disease corpus, a collection of 793 PubMed
abstracts fully annotated at the mention and concept level to serve as a research resource for the biomedical natural
language processing community. Each PubMed abstract was manually annotated by two annotators with disease mentions
and their corresponding concepts in Medical Subject Headings (MeSH®) or Online Mendelian Inheritance in Man (OMIM®).
Manual curation was performed using PubTator, which allowed the use of pre-annotations as a pre-step to manual annotations.
Fourteen annotators were randomly paired and differing annotations were discussed for reaching a consensus in two
annotation phases. In this setting, a high inter-annotator agreement was observed. Finally, all results were checked
against annotations of the rest of the corpus to assure corpus-wide consistency.
For more details, see: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951655/
The original dataset can be downloaded from: https://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/DISEASE/NCBI_corpus.zip
This dataset has been converted to CoNLL format for NER using the following tool: https://github.com/spyysalo/standoff2conll
Note: there is a duplicate document (PMID 8528200) in the original data, and the duplicate is recreated in the converted data.pubmedNLM produces a baseline set of MEDLINE/PubMed citation records in XML format for download on an annual basis. The annual baseline is released in December of each year. Each day, NLM produces update files that include new, revised and deleted citations. See our documentation page for more information.MedCalc-Bench
[!Note]
Please visit MedCalc-Bench Verified at this url: https://github.com/nikhilk7153/MedCalc-Bench-Verified for the latest changes. Here is the HuggingFace link: https://huggingface.co/datasets/nsk7153/MedCalc-Bench-Verified.
The first version of MedCalc-Bench Verified is an update from v1.2 on this repository.
MedCalc-Bench is the first medical calculation dataset used to benchmark LLMs ability to serve as clinical calculators. Each instance in the dataset consists of a patient note, a… See the full description on the dataset page: https://huggingface.co/datasets/ncbi/MedCalc-Bench.MedCalc-Bench-v1.2
[!note]
Please visit MedCalc-Bench Verified at this url: https://github.com/nikhilk7153/MedCalc-Bench-Verified for the latest changes. Here is the HuggingFace link: https://huggingface.co/datasets/nsk7153/MedCalc-Bench-Verified.
The first version of MedCalc-Bench Verified is an update from v1.2 on this repository. We recommend using v1.0-v1.2 for reproducibility purposes only. You should specify which version you are using when using this dataset.
MedCalc-Bench is the first medical… See the full description on the dataset page: https://huggingface.co/datasets/ncbi/MedCalc-Bench-v1.2.